1qp7

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[[Image:1qp7.gif|left|200px]]
 
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==PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX==
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The line below this paragraph, containing "STRUCTURE_1qp7", creates the "Structure Box" on the page.
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<StructureSection load='1qp7' size='340' side='right'caption='[[1qp7]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1qp7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QP7 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
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{{STRUCTURE_1qp7| PDB=1qp7 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qp7 OCA], [https://pdbe.org/1qp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qp7 RCSB], [https://www.ebi.ac.uk/pdbsum/1qp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qp7 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qp/1qp7_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qp7 ConSurf].
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<div style="clear:both"></div>
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'''PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX'''
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==See Also==
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*[[Purine repressor|Purine repressor]]
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== References ==
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==Overview==
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<references/>
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The interaction of the dimeric Escherichia coli purine repressor (PurR) with its cognate sequences leads to a 45 degrees to 50 degrees kink at a central CpG base step towards the major groove, as dyad-related leucine side-chains interdigitate between these bases from the minor groove. The resulting broadening of the minor groove increases the accessibility of the six central base-pairs towards minor groove interactions with residues from PurR. It has been shown that lysine 55 of PurR makes a direct contact with the adenine base (Ade8) directly 5' to the central CpG base-pair step in the high-affinity purF operator sequence. We have investigated the importance of this interaction in the specificity and affinity of wild-type PurR (WT) for its operators and we have studied a mutant of PurR in which Lys55 is replaced with alanine (K55A). Complexes of WT and K55A with duplex DNA containing pur operator sequences varied at position 8 were investigated crystallographically, and binding studies were performed using fluorescence anisotropy. The structures of the protein-DNA complexes reveal a relatively unperturbed global conformation regardless of the identity of the base-pair at position 8 or residue 55. In all structures the combination of higher resolution and a palindromic purF operator site allowed several new PurR.DNA interactions to be observed, including contacts by Thr15, Thr16 and His20. The side-chain of Lys55 makes productive, though varying, interactions with the adenine, thymine or cytosine base at position 8 that result in equilibrium dissociation constants of 2.6 nM, 10 nM and 35 nM, respectively. However, the bulk of the lysine side-chain apparently blocks high-affinity binding of operators with guanine at position 8 (Kd620 nM). Also, the high-affinity binding conformation appears blocked, as crystals of WT bound to DNA with guanine at position 8 could not be grown. In complexes containing K55A, the alanine side-chain is too far removed to engage in van der Waals interactions with the operator, and, with the loss of the general electrostatic interaction between the phosphate backbone and the ammonium group of lysine, K55A binds each operator weakly. However, the mutation leads to a swap of specificity of PurR for the base at position 8, with K55A exhibiting a twofold preference for guanine over adenine. In addition to defining the role of Lys55 in PurR minor groove binding, these studies provide structural insight into the minor groove binding specificities of other LacI/GalR family members that have either alanine (e.g. LacI, GalR, CcpA) or a basic residue (e.g. RafR, ScrR, RbtR) at the comparable position.
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__TOC__
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</StructureSection>
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==About this Structure==
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1QP7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QP7 OCA].
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==Reference==
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The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions., Glasfeld A, Koehler AN, Schumacher MA, Brennan RG, J Mol Biol. 1999 Aug 13;291(2):347-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10438625 10438625]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Brennan, R G.]]
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[[Category: Brennan RG]]
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[[Category: Glasfeld, A.]]
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[[Category: Glasfeld A]]
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[[Category: Koehler, A N.]]
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[[Category: Koehler AN]]
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[[Category: Schumacher, M A.]]
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[[Category: Schumacher MA]]
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[[Category: Dna-binding]]
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[[Category: Purine biosynthesis]]
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[[Category: Repressor]]
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[[Category: Transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 06:32:40 2008''
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Current revision

PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

PDB ID 1qp7

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